Retrained
by Light8mare
Summary: It's been two years since John was last seen. He's just been found. When it becomes clear that the retraining of Sherlock's "pet" has left both physical and mental scars, how will Sherlock cope with his flatmates odd changes in behavior and personality?
1. Chapter 1

**First Sherlock fanfic for me to officially put into existence. **

**Yay. Clap for me. Don't own and the like.**

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The feeling of the soles of his shoes hitting the tile only proved to urge him on, reminding him that there was a _very _important reason for his haste.

Every smack against the floor was another dark image dredged up by his imagination.

It was thrusting even more adrenaline into his system and making him frantic.

He could distantly hear someone, Lestrade, speaking very loudly at him, trying to make him calm down.

He couldn't calm down. No.

There was no way Sherlock could possibly consider coming off his sudden giddy state.

Because John was _alive! _John was _here!_

And there was nothing was going to stop Sherlock Holmes from seeing him.

It was only after finally standing in the doorway where John was in clear view did he stop. He felt Lestrade stumble behind him, caught off by the sudden halt, but he dismisses it as unimportant.

What was important was the man laying unconscious in the hospital bed.

For anyone else, that moment would have been chock full of emotion, complete with a breakdown and running forward to clutch his hand, sobbing about how much he was missed.

However, Sherlock felt no inclination to do so. Whether he was or wasn't really a sociopath, it was clear his ability to love was quite maldeveloped. John was his best friend. One of the few people Sherlock took a liking to, but his way of caring was different. It was more possessive, more material.

John was one of _his _people, and Sherlock wanted to keep his things safe.

And now, for the first time in more than two years, Sherlock could content himself with the knowledge that what was his was not in immediate danger.

Not physically anyway. The state of his mentality remained unsure. He'd been unconscious when he had been found after all.

Sherlock guessed it had something to do with his back. The flesh was, after all, utterly mutilated into a mess of twisted knots of scars and infected tears. The state of the rest of his body wasn't much better. It looked too painful to imagine him moving without burning agony, which certainly explained the fetal position he had claimed.

Sherlock wondered vaguely if the marks marring his face would heal and fade eventually. It didn't look like they would.

"Sherlock?" Lestrade's carefully toned question reminds him that the rest of the world unfortunately still existed (although he did like Mrs. Hudson... And Mycroft had his uses... Maybe if they just did away with the annoying people like Anderson it would be ok) and that he had been standing in the doorway staring at John for several minutes now.

With a "hn," he moves to sit down by the bed, consequently allowing others access into the room. Disdainfully, he ignores them, instead focusing on John. He wonders if light physical interaction will cause him to wake up. Wanting to test the theory, Sherlock very gently slides his fingers around John's, watchful of the bruises and cuts, and blatantly chooses to ignore the consideration of what this may look like to another person.

_"People will talk."_

He had always found everything about people's talk annoying until it had become a bit of an inside joke between them.

Now the thought made him angry, because John wasn't conscious to lift the mood.

Because he was in pain. Because Sherlock had been incapable of keeping him from it. It was Sherlock's fault.

"Sherlock." He turns and faces Lestrade, not wanting to talk and making such clear on his face.

"It's been two full years since he was free... And, well, the doctors think that he may not be quite the same-"

"Of course I already know that! It's only totally _obvious_ that this will have negative effects on him! Not many people can pull through two full _bloody years _of tort-" He cuts off at the feeling of movement. Once again focusing all attention on John, he watches the man as his muscles and face twitch in the start of waking.

Then his eyes open.

Sherlock studies those wide muddy blues, the ones that were just so tinted that it was difficult to distinguish the exact color, as they drowsily begin to adjust.

John was there, right? That was John in those eyes, right?

"John?"

Slowly, every movement made sluggish by sedatives and pain killers, John meets Sherlock's eyes.

It's like meeting a wall.

John's eyes were normally very much open and genuine, fitting his character and skill to lie (or lack of thereof). These eyes, however, are murky and shadowed.

"John, you're awake." Sherlock resists the urge to point out how downright obvious Lestrade's comment is, instead choosing to watch John as he turns at the sound of the noise.

"Hey. S'been a while," Lestrade says with a smile. John just stares for a moment before letting his gaze drift around the room, taking in his surroundings. "You, uh..." Lestrade swallows his awkwardness and continues, "You've been rescued. You're in a hospital now."

John doesn't seem interested in what he's saying, continuing to scan his new environment.

Why was his expression so... Blank? It was odd, and a bit unsettling. "John." A light squeeze of his fingers brings the muddy blues back to examine the person so nearby. "John, can you talk to us?" Sherlock asks, wanting to confirm that he's not been rendered mute by either psychological or physical damage.

John, however, has seemed to have grown pale and has begun to shiver softly. Of course. He's still weak.

"Go back to sleep then, " Sherlock tells him, but he's already shut his eyes. Its only moments later that his breathing evens slightly.

Everyone in the room is quiet for a while, each trying to correct the assuming thought perking in their minds.

"It's still too early to tell," Lestrade suggests helpfully.

"Yeah..." Everyone tries to cling to that excuse. Its unfortunate, however, that doubt it so hard to quell.


	2. Chapter 2

Being in the flat had become bearable again.

When they had still been uncertain, still searching, the flat had seemed to throw a tantrum without it's John. No experiments had gone right, Sherlock had lost things constantly, and that _silence _was deafening.

Apparently the flat was just as possessive as Sherlock.

Now that the news had gotten out, the atmosphere was free of its crushing tension. It was for this reason that Sherlock chose against his new habit of sleeping on benches, Lestrade's couch, or whatever hotel room Mycroft had gotten for him on the bad nights that were the only time he willing accepted his help, and actually slept in his own bed.

Or at least, tried to. Nightmares kept chasing him in circles around his mind, causing his to wake frequently. What really annoyed him to no end, however, was the irrational fear and emotion at the scenes painted by his grim subconscious. It didn't seem to matter that he was a steel-nerved, gore-desensitized, sociopathic man of _logic_, his dreams showed off H.O.U.N.D drug-like attributes and overrode everything.

Their sudden need to perform such stunts strangely happened to coincide directly after seeing John again. How odd. It couldn't be that he was... _Worried_ about John... Right?

_Well, _he concludes, _It isn't completely ridiculous. After all, he is hurt. Very badly so. And possibly psychologically damaged as well. So concern is justified, _he reassures himself. And of course he cares because John is _his_. He didn't allow these things to happen to his people because it changed them and made them... _needy. _

Needy people were not his forte.

Still, it didn't change how exhausting this 'caring' was. He'd been feeling the strain of sleep deprivation long before this, so this nightmare drama and worrying business was more than a nuisance to him.

It was during the aftermath of one of these dreams that a phone call split the quiet of the flat.

"Hello?" Sherlock tries to keep the annoyance out of his voice, but its a doomed attempt.

"Is this Sherlock Holmes?" A female voice asks.

"Who wants to know?"

"The hospital holding John Watson."

Immediately, Sherlock has to shove away dark images painted by his mind. "How is he?"

"He was doing just fine up until now. He was on sedatives, so he's been asleep for the majority of the time, but when he woke up thirty minutes ago he became extremely upset for no apparent reason. When nurses attempted to calm him down, it only proved to agitate him further to the point where we are concerned he'll hurt himself."

"And?"

"We're hoping a familiar face will help calm him enough to sedate him again. We can't allow him to worsen his injuries."

Of course. No doubt he had already reopened several of them if he is as uncontrollable as she says.

"I'll be there," Sherlock assures her. When she hangs up, he rushes to get dressed.

.£.

"Did you contact his sister Harry?"

"No," the nurse answers as she jogs to keep pace with him. It was a different one than before, with a higher voice and more energy. Probably had only been here a month or two, but she seemed professional enough to ensure that she had plenty of previous experience, so she had likely just been transfered to this hospital from a different one.

"Why not?" Sherlock asks.

"She wasn't on his emergency contacts. It was just you and Lestrade."

_So John doesn't trust her enough to care for another person. A logical decision, she _is_ an alcoholic so it may be questionable whether she can even care for just herself. Though I admit I'm curious about his choices. Lestrade isn't exactly a close friend of his, and I'm not really the "caring type". There are no others on there so clearly he doesn't have any other close living family, and he has no other friends he trusts. Odd, I thought he and Mike were friends. Apparently its not a relationship that goes beyond familiarity and polite friendliness. Those aren't uncommon for John._

They stop in front of a door, the same one Sherlock stood in just yesterday, and Sherlock listens for any hint of action behind it.

It's silent.

The nurse begins to give him advice on how to approach John, but Sherlock ignores her and goes ahead to turn the knob.

He peers inside cautiously. When there's no reaction to his entry, he slips inside and shuts the door behind him. If things turned bad, he didn't want to give John the ability to escape.

He has to squint as he searches in the darkness for the doctor, but he finally spots John's smaller figure hunched up against the corner walls. Stepping over a fallen IV stand, likely toppled in the scuffle that brought him here, Sherlock slowly moves closer.

"John?" He tries again, keeping his voice low. John doesn't give any noticeable response to it so Sherlock kneels down a few feet away. From here its easier to see the way the hospital uniform hangs in folds off his malnourished frame. The lack of weight on his already weakened body left him defenseless to the cool hospital air, making John shiver excessively.

The skin on his neck still had an irritated red ring encircleing all the way around along with several purple splotches dotting it. The collar on the uniform hung down low enough to reveal ends of burns and lacerations peeking from under bandages on his chest. Every breath hitches into an agony filled sob that John is clearly struggling to repress. The pain of his wounds must have elevated immensely from all the movement, and being pressed into the wall was only going to worsen it.

"John," he murmers and slowly reaches forward. "I'm going to touch you, alright?"

His fingers brush the side of John's hand, wary of the scabby scratches crisscrossing over the flesh. The flinch is so small and well suppressed that if he hadn't been watching as closely as he had, Sherlock would have missed it.

Careful not to move too fast for his unstable flatmate, Sherlock lightly slides his hand under John's fingers. By now he can taste the tension in the air. If Sherlock can't get John back to his bed and calmed down, there's danger of a worse meltdown. "Can you stand with me?"

The question wasn't just about his mental state, but about his physical was well. His feet had gashes running through the bottoms of them and the flesh was raw and sore. No doubt getting him to put weight on them was a bad idea, but there weren't any better options. Even carrying him would agrivate more injuries.

Sherlock asks again silently with a soft tug on his finger tips. Its several moments before John responds, but his fingers curl ever so slightly around Sherlock's in an affirmation.

Sherlock eases up from his position in a gradual way, letting John take his time in following. Every step is slow and stiff, and his back curls inwards as he represses murmers of pain. The short walk back to the bed is far tenser than it should be, and when they reach it John halts abruptly.

"John, you need to get back in bed." Sherlock tells him but John stiffens. "Really John. I'm serious. You _need _to get back in bed. Its important for you to rest now." John pulls his hand from Sherlock and huddles into himself, backing away slightly.

Not good. He was being upset by something. The bed? He'd been fine earlier, back when Lestrade and the others had come it, although he had gotten pale. What was a difference here? Could it be the dark maybe?

Sherlock strides to the light switch, then hesitates. If he wasn't right, the shock of the light could cause John to panic even worse. A risk he'd have to take, as John was becoming worse anyways.

With a flick, the room fills with warm light.

John flinches at the flash, though does nothing more besides squint and blink rapidly to adjust his eyes. Sherlock walks back towards him, one careful step at a time, but he doesn't react.

"John?"

His flatmate rolls his weight uncomfortably over his obviously stinging feet and gazes around the room, apparently more at ease now.

So it _was_ the darkness. John had never displayed any hint of that fear previously, so it was a new thing. Anger flares in Sherlock's stomach again. He was _really _beginning to hate whoever had done this. Vaguely, he wonders if his harpoon was still under the couch. He may be needing it should he find those responsible.

Sherlock touches John's hand again and blank dark eyes stare through his. "Will you go to bed now?" Sherlock asks him quietly. John's attention shifts away again and his eyes lazily continue to roam the room, not at all showing signs of even understanding the question. When Sherlock tugs, he follows passively, and John allows himself to be returned to the mattress without further struggle.

Sherlock opens the door and quietly warns the nurses against turning off the lights, then steps out, though hesitates to watch them as they set up the IV again. John's eyes were shut tightly. His muscles had tightened instinctively against the harsh throbbing of his wounds.

He wasn't the same. John wasn't John anymore. He was just a shivering stranger in a too-white hospital who couldn't even face a darkened room. He had become like this because of Sherlock's failure in retrieving him.

It gave rise to strange feelings in his stomach that the consulting detective didn't like.

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**Don't worry. It gets better.**

**At least from my perspective. Which isn't a good one. **

**So you can expect worse for dear John.**

**Review! **


	3. Chapter 3

"Why are you here?"

Mycroft just smiles at him. "Merely concerned for you. Is that alright?"

"No, it's not. You've never been this worried when _I _was in the hospital. For what reason are you now?"

Mycroft twirls his umbrella and shifts. "Oh, I think there are plenty. Shall I start with the mildest?" He takes Sherlock's silence as a go-ahead and continues, "You've been at this hospital all night. Not only has this affected your health and judgment, but it's unusual for you and warrants my attention. You haven't eaten properly since three weeks ago when I forced you, and you now appear to be rejecting food again, much like you do when on a case."

"You are not planning on taking care of basic hygiene since it is too 'inconvenient' at the moment and you look a wreck. You are not planning on taking any cases, including the one Detective Inspector Lestrade is about to phone you about as you are too wound up with this. You are angry and want to hurt someone, preferably the people who harmed John, and you are concerned about John's mental state as it is no longer something you understand and can balance. How far this whole matter has fallen from your hands has made you feel incapable and irritated, but what's worse is that as prime health contact, flatmate, and 'best friend' it is technically your duty to help 'fix' John, which has made you uneasy and has given you the odd feeling of being... Unqualified."

"Of course not!" Sherlock snaps angrily.

"And why not?! Admit it brother, you have absolutely no idea in the slightest on how to care for someone as needy and dependant as a thoroughly traumatized torture victim." His eyes narrow. "You're over your head just considering it. I suggest you-"

"I _what, _Mycroft? Step back? Let someone else handle him? He has _no one _else!"

"No Sherlock, not exactly. I meant that you should let someone more capable take care of him," Mycroft says sternly. "I know a few select professionals who could-"

"No Mycroft! That won't help him and you know it! You'd just be alienating him from what he knows," Sherlock snaps. "He'll just get worse. He needs-"

"How would you know what he needs?" Mycroft asks, enunciating it carefully as if speaking to someone less intelligent. "You can't even decipher his emotional process when he's sane so _let me help you._"

"Lestrade will help me. And Mrs. Hudson," Sherlock decides firmly.

"Ah," Mycroft counters. "But how much 'help' will they be? The Detective Inspector doesn't have a lot of time on his hands with his job, and Mrs. Hudson is just an elderly landlady. You cannot possibly expect her to be of much help. Face it Sherlock, he needs help that you can't give."

"_You _can't give it either! The only reason you're doing this is so I won't be affected by him, isn't that right?"

"Caring _isn't _an advantage Sherlock. Isn't that what I've told you? And now look at yourself."

"Mycroft, I am _fine._"

"We both know that isn't true."

" I am! And I'm perfectly capable of handling John _without _your 'assistance'!"

"Denial proves nothing brother."

Sherlock angrily grabs a basket of pens and throws them at Mycroft hard. "_Get out!_"

Mycroft easily dodges them, then turns to leave. "I'll be monitoring your 'handling' of the situation. My offer will remain open." And then he's gone.

Sherlock remains on his feet, fuming until a nurse tells him he's allowed to go into John's room.

John's eyes are half-lidded and glazed, a clear effect of the medication he's on, but he's still able to turn his gaze towards Sherlock.

Sherlock shifts uneasily. What did one say to someone in John's state? 'Good morning' seemed a little out of place.

His phone buzzes in his pocket, likely the call from Lestrade predicted by his brother. The reminder of their argument sparks Sherlock to move, wanting to disprove Mycroft.

He steps a foot or two closer and hesitates before commenting, "you're looking... Not as bad."

John's eyes drift from his, losing focus just as easily as he had in their last recent meetings. With a sigh, Sherlock grabs a chair and sits next to the bed. "How are you?" He tries.

His flatmate continues to ignore his existence in favor of studyinging a collection of medical tools on a counter across the room and Sherlock finally, losing his patience, presses both hands on either side of John's head and guides him back to face him. John's only response is to stiffen uncomfortably, but he makes the effort to struggle to focus on Sherlock's eyes after a moment.

"Listen to me John, I know you're in a bad way from what's been done to you, but I need you to listen," Sherlock starts. "We have to know who did this to you so we can catch them. You don't want them to hurt other people, correct? Of course not. So I _need_ you to remember. You have to tell me."

John shuts his eyes tightly and tries to pull away.

"John-" Sherlock cuts off when two hands softly press on his chest, pushing him back.

Somehow he had discomforted John with his actions already. Was he being too blunt? Was it his timing? Those were usually his two main failures with emotionally imbalanced people. Either way, he was clearly supposed to back off.

Sherlock settles back against the chair with a sigh. That information was important. But he had to take care of John first.

Glancing his way, he notices that John had gotten shivery again. "I... I'm supposed to take care of you now... I think," Sherlock tells him, wanting to make sure John was told before he fell asleep again.

John simply watches him drowsily, either not understanding or not caring about the information.

.£.

Mrs. Hudson greets him with a smile when he walks through the door.

"Oh, hello dear! I didn't expect you back!" Her expression sombers slightly and she adds, "It isn't about John right?"

"No Mrs. Hudson, John's... Well, he's as well as can be expected." He assures and goes upstairs to the flat.

Human nature was not his specialty. He didn't know how to fix a broken person, he was a detective for heaven's sake! Not a bloody psycologist!

How the heck was he supposed to manage this?

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**If there are any Brits out there that want to correct my silly American ignorance in any subject, feel totally free.**

**Actually, any readers who feel my writing failing, feel free to critique and help. I can't keep ideas straight in my head and they come out all weird in writing, so I'm bound to have a few spots that deteriorate.**

**Also, any ideas for odd behavior? I have a few, but suggestions are completely welcome. **


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